Investigation of Scrambled Ions in Tandem Mass Spectra Part 1: Statistical Characterization

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Investigation of Scrambled Ions in Tandem Mass Spectra Part 1: Statistical Characterization

Journal Name: Journal of the American Society for Mass Spectrometry

Naiping Dong, Liangxiao Zhang, Yizeng Liang*

College of Chemistry and Engineering, Central South University, Changsha 410083, P. R. China.

E-mail for Corresponding Author:

Supplementary Material

Figure S-1. Length of primary ions versus length of peptides...... S2

Figure S-2. Average intensity of scrambled ions as a function of length of primary ion...... S4

Figure S-3.Fraction of residues occurring scramble reactions...... S3

Figure S-4. Average intensity of scrambled ions when peptides absent residues…...... ………….... S5

Figure S-5. Fraction of scrambled ions when peptides absent residues...S6

Figure S-6. Fraction of scrambled ions versus peptide length...... S7

Figure S-7. XCorr versusfraction of scrambled ions...... S9

Figure S-8. Fraction of scrambled ionsand sequential ions versus peptide length...... S14

Figure S-1.Distribution of length of preliminary sequential ions (b anda type ion) that produce scrambled ions versuslength of precursor peptides ions at +1, +2, +3 and +4 charge state.

Figure S-2. Average normalized intensity of scrambled ions as a function of length of the primary ion in tandem mass spectra generated by singly (+1), doubly (+2), triply (+3) and quadruply (+4) charged precursor ions.

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B

Figure S-3. Fraction of occurring reopening reaction (A)and cleavage (B) at C-terminal and N-terminal side of each amino acid ina ions. Single letter code residues listed in the lowermost row correspond to residues.

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Figure S-4.Average intensity of scrambled b (A) and a (B) ions produced by peptides absent residues listed along X axis.

Figure S-5. Number fraction of scrambled ions produced by peptides which absent residues listed along X axis.

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Figure S-6.Fraction of scrambled ions as a function of peptide length for false and true identifications at different charge states. The data were generated by linear ion trap platform (A), MALDI-TOF-TOF platform (B) and QTOF (C) platform.

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Figure S-7. XCorr versusfraction of scrambled ions. Fraction of scramble ions is calculated by number of scramble ions in a spectrum versus total peak number of the spectrum.Data were generated on A: 3D ion trap platform, singly charged; B: 3D ion trap platform, doubly charged; C: 3D ion trap platform, triply charged; D: linear ion trap platform, singly charged; E: linear ion trap platform, doubly charged; F: linear ion trap platform, triply charged; G: QTOF platform, singly charged; H: QTOF platform, doubly charged; I: QTOF platform, doubly charged; J: MALDI-TOF-TOF platform.

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Figure S-8. Number fraction of scrambled ions and sequential ions for in falsely identified and correctly identified dataset as a function of peptide length. Data were generated on A-C: 3D ion trap platform, by singly,doubly and triply charged precursors; D-F: QTOF platform, by singly, doubly and triply charged precursors; G: MALDI-TOF-TOF platform, by singly charged precursors; H-J: linear ion trap platform, by singly, doubly and triply charged precursors.